Research / Simulation Corpus / Tier 1 Reports

Tier 1 simulation reports

Representative journal-style simulation reports, one per major phase cohort, grounded in the Tier 1 structural record.

Section: ResearchEpistemic status: formalLast updated: February 11, 2026

MF-SIM-001 - AND Gate

Phase: Phase I - Logic Primitives

Hypothesis: A dual-input strand displacement architecture produces output only when both inputs are present.

Simulation topology: Two exposed toeholds (t1, t2) gate a protected output domain; full branch migration requires both inputs.

What was tested: All four Boolean input combinations.

What passed: Truth-table equivalence and no output under single/null input conditions.

Constraints required: Orthogonal toehold domains and intended reaction-rate dominance over leak pathways.

Scaling boundary observed: Leak sensitivity increases with reduced orthogonality and deeper cascade layering.

MF-SIM-010 - 1-bit Delay Element

Phase: Phase II - Temporal Behavior

Hypothesis: Delay is controllable through toehold modulation under bounded concentration constraints.

Simulation topology: Input-triggered delay block with release controlled by kinetic tuning variables.

What was tested: Delay behavior under bounded trigger windows and fixed hierarchy constraints.

What passed: Ordered delayed release behavior remained structurally consistent in bounded regimes.

Constraints required: Rate hierarchy separation and concentration envelopes required.

Scaling boundary observed: Timing variance increases with chained temporal elements.

MF-SIM-017 - 1-bit RAM Cell

Phase: Phase IIIA - Memory Architectures

Hypothesis: Persistent rewritable memory is achievable in displacement-based architecture.

Simulation topology: Protected memory domain with write, read-enable, and overwrite pathways.

What was tested: State retention and controlled overwrite under bounded assumptions.

What passed: Persistent state retention and explicit overwrite behavior observed structurally.

Constraints required: Memory gate pathway dominance and orthogonality of memory-associated domains.

Scaling boundary observed: Additional memory gating layers increase leak-risk surfaces.

MF-SIM-020 - Enable-Gated Branch Structure

Phase: Phase IIIB - Control Logic

Hypothesis: Conditional branch activation can remain exclusive under valid gate conditions.

Simulation topology: Enable gate controlling mutually exclusive branch output paths.

What was tested: Branch activation under valid/invalid gate combinations.

What passed: Exclusive branch behavior preserved in bounded model assumptions.

Constraints required: Strict gate dominance and branch orthogonality.

Scaling boundary observed: Path exclusivity sensitivity increases in dense branch topologies.

MF-SIM-023 - 4-bit Ripple Carry Adder

Phase: Phase IIIC - Arithmetic Units

Hypothesis: Sequential carry propagation can be achieved through displacement cascades.

Simulation topology: Bitwise add stages with carry handoff between successive gates.

What was tested: Carry progression across multi-stage arithmetic chain.

What passed: Structural carry propagation preserved under bounded depth assumptions.

Constraints required: Sequential trigger ordering and reaction-rate hierarchy.

Scaling boundary observed: Cumulative latency grows with arithmetic depth.

MF-SIM-026 - Latency Stacking Analysis

Phase: Phase IV - Timing and Coordination

Hypothesis: Cumulative delay remains bounded under coordinated multi-stage execution.

Simulation topology: Three-stage cascaded gates with aggregated delay evaluation.

What was tested: Total latency accumulation across sequential activation stages.

What passed: Coordinated sequence remained structurally stable in bounded windows.

Constraints required: Bounded diffusion/kinetic assumptions and trigger ordering.

Scaling boundary observed: Delay variance amplifies as stage count increases.

MF-SIM-031 - Sequential Trigger Chain

Phase: Phase V-VI - Environmental I/O and Sequencing

Hypothesis: Ordered execution can be maintained in externally influenced runtime progression.

Simulation topology: External signal-driven cascade with sequential state transitions.

What was tested: Stepwise state transitions with conditional branching checkpoints.

What passed: Ordered progression held under bounded signal and timing assumptions.

Constraints required: Trigger availability ordering and threshold-gated transitions.

Scaling boundary observed: Instruction ordering sensitivity grows with branching complexity.

MF-SIM-038 - Global Macrostate Convergence

Phase: Phase VII-VIII - Compiler Mapping and Integration

Hypothesis: Integrated system converges deterministically across coupled subsystems.

Simulation topology: Linked logic, memory, arithmetic, control, and runtime blocks with shared output macrostate.

What was tested: End-to-end convergence consistency under integrated conditions.

What passed: System-level structural convergence observed under bounded constraints.

Constraints required: Cross-subsystem consistency and preserved reaction hierarchy.

Scaling boundary observed: Global convergence margin narrows near upper cascade-depth assumptions.

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